[2024-01-24 14:11:46,683] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:46,685] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:46,685] [INFO] DQC Reference Directory: /var/lib/cwl/stg8efe817e-0f93-4abb-bfc0-c21270e9e3c3/dqc_reference
[2024-01-24 14:11:47,883] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:47,884] [INFO] Task started: Prodigal
[2024-01-24 14:11:47,884] [INFO] Running command: gunzip -c /var/lib/cwl/stg3501792b-a93a-4565-8052-75f28fb6895b/GCF_003355455.1_ASM335545v1_genomic.fna.gz | prodigal -d GCF_003355455.1_ASM335545v1_genomic.fna/cds.fna -a GCF_003355455.1_ASM335545v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:11:58,159] [INFO] Task succeeded: Prodigal
[2024-01-24 14:11:58,159] [INFO] Task started: HMMsearch
[2024-01-24 14:11:58,159] [INFO] Running command: hmmsearch --tblout GCF_003355455.1_ASM335545v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8efe817e-0f93-4abb-bfc0-c21270e9e3c3/dqc_reference/reference_markers.hmm GCF_003355455.1_ASM335545v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:11:58,425] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:11:58,426] [INFO] Found 6/6 markers.
[2024-01-24 14:11:58,457] [INFO] Query marker FASTA was written to GCF_003355455.1_ASM335545v1_genomic.fna/markers.fasta
[2024-01-24 14:11:58,457] [INFO] Task started: Blastn
[2024-01-24 14:11:58,457] [INFO] Running command: blastn -query GCF_003355455.1_ASM335545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8efe817e-0f93-4abb-bfc0-c21270e9e3c3/dqc_reference/reference_markers.fasta -out GCF_003355455.1_ASM335545v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:11:59,306] [INFO] Task succeeded: Blastn
[2024-01-24 14:11:59,310] [INFO] Selected 17 target genomes.
[2024-01-24 14:11:59,310] [INFO] Target genome list was writen to GCF_003355455.1_ASM335545v1_genomic.fna/target_genomes.txt
[2024-01-24 14:11:59,342] [INFO] Task started: fastANI
[2024-01-24 14:11:59,342] [INFO] Running command: fastANI --query /var/lib/cwl/stg3501792b-a93a-4565-8052-75f28fb6895b/GCF_003355455.1_ASM335545v1_genomic.fna.gz --refList GCF_003355455.1_ASM335545v1_genomic.fna/target_genomes.txt --output GCF_003355455.1_ASM335545v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:10,102] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:10,102] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8efe817e-0f93-4abb-bfc0-c21270e9e3c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:10,102] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8efe817e-0f93-4abb-bfc0-c21270e9e3c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:10,117] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:12:10,117] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:12:10,117] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	82.2402	634	1123	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	81.6876	613	1123	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	81.5695	604	1123	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	81.089	523	1123	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	80.9537	531	1123	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	80.8487	532	1123	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	80.8461	536	1123	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	80.7914	540	1123	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	80.7424	537	1123	95	below_threshold
Qipengyuania pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	80.6911	541	1123	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	80.6207	552	1123	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	80.4938	494	1123	95	below_threshold
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	80.4724	513	1123	95	below_threshold
Qipengyuania aquimaris	strain=JCM 12189	GCA_009827445.1	255984	255984	suspected-type	True	80.3949	485	1123	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	77.7553	203	1123	95	below_threshold
Sphingomonas kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	77.7375	234	1123	95	below_threshold
Allopontixanthobacter sediminis	strain=KCTC 42453	GCA_009828115.1	1689985	1689985	type	True	77.7184	309	1123	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:10,119] [INFO] DFAST Taxonomy check result was written to GCF_003355455.1_ASM335545v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:10,119] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:10,119] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:10,120] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8efe817e-0f93-4abb-bfc0-c21270e9e3c3/dqc_reference/checkm_data
[2024-01-24 14:12:10,121] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:10,156] [INFO] Task started: CheckM
[2024-01-24 14:12:10,156] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003355455.1_ASM335545v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003355455.1_ASM335545v1_genomic.fna/checkm_input GCF_003355455.1_ASM335545v1_genomic.fna/checkm_result
[2024-01-24 14:12:45,046] [INFO] Task succeeded: CheckM
[2024-01-24 14:12:45,047] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:12:45,067] [INFO] ===== Completeness check finished =====
[2024-01-24 14:12:45,068] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:12:45,068] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003355455.1_ASM335545v1_genomic.fna/markers.fasta)
[2024-01-24 14:12:45,069] [INFO] Task started: Blastn
[2024-01-24 14:12:45,069] [INFO] Running command: blastn -query GCF_003355455.1_ASM335545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8efe817e-0f93-4abb-bfc0-c21270e9e3c3/dqc_reference/reference_markers_gtdb.fasta -out GCF_003355455.1_ASM335545v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:46,470] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:46,475] [INFO] Selected 16 target genomes.
[2024-01-24 14:12:46,475] [INFO] Target genome list was writen to GCF_003355455.1_ASM335545v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:12:46,507] [INFO] Task started: fastANI
[2024-01-24 14:12:46,508] [INFO] Running command: fastANI --query /var/lib/cwl/stg3501792b-a93a-4565-8052-75f28fb6895b/GCF_003355455.1_ASM335545v1_genomic.fna.gz --refList GCF_003355455.1_ASM335545v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003355455.1_ASM335545v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:12:57,262] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:57,281] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:12:57,281] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_003355455.1	s__Qipengyuania aurea	100.0	1123	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.67	97.64	0.83	0.82	3	conclusive
GCF_001542855.1	s__Qipengyuania sp001542855	84.3294	715	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCA_016764075.1	s__Qipengyuania sp016764075	82.6575	488	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828015.1	s__Qipengyuania citrea	82.4298	652	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.91	97.49	0.87	0.80	20	-
GCF_011762005.1	s__Qipengyuania flava	82.2247	636	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.04	96.57	0.91	0.85	10	-
GCF_009827315.1	s__Qipengyuania gaetbuli	80.8431	535	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015767595.1	s__Qipengyuania sp002895025	80.7387	540	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.29	96.55	0.87	0.78	16	-
GCA_000756795.1	s__Qipengyuania vulgaris_A	80.6546	523	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115585.1	s__Qipengyuania nanhaisediminis	80.4855	511	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827445.1	s__Qipengyuania aquimaris	80.3896	485	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248395.1	s__Qipengyuania sp003248395	79.8759	403	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177715.1	s__Erythrobacter xiamenensis	79.5724	424	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641735.1	s__Sphingomonas metalli	77.8162	204	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828115.1	s__Pseudopontixanthobacter_A sediminis	77.7293	308	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204495.1	s__Sphingomonas kyeonggiensis_A	77.5474	226	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000281975.1	s__Novosphingobium sp000281975	77.4291	272	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:12:57,283] [INFO] GTDB search result was written to GCF_003355455.1_ASM335545v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:12:57,284] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:12:57,288] [INFO] DFAST_QC result json was written to GCF_003355455.1_ASM335545v1_genomic.fna/dqc_result.json
[2024-01-24 14:12:57,288] [INFO] DFAST_QC completed!
[2024-01-24 14:12:57,288] [INFO] Total running time: 0h1m11s